ArticleDatabase : the journal of biological databases and curation2013
Using the OntoGene pipeline for the triage task of BioCreative 2012.
Article in Database : the journal of biological databases and curation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
10 citing papers in PubMed.
- Article
- Strategies towards digital and semi-automated curation in RegulonDB.Database : the journal of biological databases and curation · 2017Article
- Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis.Database : the journal of biological databases and curation · 2017Article
- Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD).Database : the journal of biological databases and curation · 2017Article
- Biocuration with insufficient resources and fixed timelines.Database : the journal of biological databases and curation · 2015Article
- Scaling drug indication curation through crowdsourcing.Database : the journal of biological databases and curation · 2015Article
- OntoGene web services for biomedical text mining.BMC bioinformatics · 2014Article
- Web services-based text-mining demonstrates broad impacts for interoperability and process simplification.Database : the journal of biological databases and curation · 2014Article
- Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12.Database : the journal of biological databases and curation · 2014Article
- BioC: a minimalist approach to interoperability for biomedical text processing.Database : the journal of biological databases and curation · 2013Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this article, we describe the architecture of the OntoGene Relation mining pipeline and its application in the triage task of BioCreative 2012. The aim of the task is to support the triage of abstracts relevant to the process of curation of the Comparative Toxicogenomics Database. We use a conventional information retrieval system (Lucene) to provide a baseline ranking, which we then combine with information provided by our relation mining system, in order to achieve an optimized ranking. Our approach additionally delivers domain entities mentioned in each input document as well as candidate relationships, both ranked according to a confidence score computed by the system. This information is presented to the user through an advanced interface aimed at supporting the process of interactive curation. Thanks, in particular, to the high-quality entity recognition, the OntoGene system achieved the best overall results in the task.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.